I'm neither smarter, nor more awake than anyone here :) but I'll throw in a couple of ideas for you:

First of all as kutsu mentioned reworking any code to fail properly and thereby probably nullify any attempt to exploit the vulnerability is the easy way to go, and as you mention, since you're willing to do it, go for it. It should not be that hard if you don't have too many files to go through.

If you look at the docs a little more in depth you'll see that not all vendors released an upgrade of Perl for this, or acknowledged it as a serious hole. Second you'll see it's a local only exploit (not remotely exploitable) so assess the risk on a system by system basis - e.g. there'll be much less risk on an application server with few if any local users. Third by the time you see any vulnerability on SecurityFocus or Regis and Kathy Lee, it's been around for ages in the wild..

It seems that in this particular case it's more important to clean up code and lock down filesystem access, and monitor your systems for unusal patterns and unauth access, along with a per-system code and user assessment, than rushing out to upgrade Perl everywhere..